PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os04g36054.1
Common NameARF9, LOC4335934, Os04g0442000, OSJNBa0064D20.11
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family ARF
Protein Properties Length: 674aa    MW: 74748.3 Da    PI: 5.7837
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g36054.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.81e-23126226198
                       EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                       f+k+lt sd++++g +++ +++aee+      ++++++ ++l+ +d++g +W +++i+r++++r++lt+GW+ Fv++++L +gD ++F   + 
  LOC_Os04g36054.1 126 FCKTLTASDTSTHGGFSVLRRHAEEClpqldmSQNPPC-QELVAKDLHGTEWHFRHIFRGQPRRHLLTTGWSVFVSSKRLVAGDAFIFL--RG 215
                       99*****************************7556666.59************************************************..44 PP

                       SEE..EEEEE- CS
                B3  88 sefelvvkvfr 98 
                       +++el+v+v+r
  LOC_Os04g36054.1 216 ESGELRVGVRR 226
                       9999*****97 PP
2Auxin_resp101.61e-33252337183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsd...ldpvrWpnSkWrsLk 83 
                       a+ha+st++ F+v+Y+Pr+s+seFvv+v+k+++a k+++svGmRfkm+fe+++++err+sGt++g+     ++ + W +S W+sLk
  LOC_Os04g36054.1 252 ASHAISTGTLFSVFYKPRTSRSEFVVSVNKYLEAKKQNLSVGMRFKMRFEGDEAPERRFSGTIIGIGSvpaMSKSPWADSDWKSLK 337
                       789*************************************************************987522267889********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.97E-45110255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.105.2E-41123241IPR015300DNA-binding pseudobarrel domain
CDDcd100171.08E-21124226No hitNo description
PROSITE profilePS5086311.533126228IPR003340B3 DNA binding domain
PfamPF023621.7E-21126226IPR003340B3 DNA binding domain
SMARTSM010191.1E-20126228IPR003340B3 DNA binding domain
PfamPF065076.4E-32252337IPR010525Auxin response factor
PfamPF023091.2E-5540583IPR033389AUX/IAA domain
PROSITE profilePS5174527.62547639IPR000270PB1 domain
SuperFamilySSF542772.16E-11549625No hitNo description
PfamPF023091.2E-7595638IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 674 aa     Download sequence    Send to blast
MAAAMEMAAN PGGSGTCSDA LFRELWHACA GPLVTVPKRG ERVYYFPQGH MEQLEASTNQ  60
QLDQYLPMFN LPSKILCSVV NVELRAEADS DEVYAQIMLQ PEADQSELTS LDPELQDLEK  120
CTAHSFCKTL TASDTSTHGG FSVLRRHAEE CLPQLDMSQN PPCQELVAKD LHGTEWHFRH  180
IFRGQPRRHL LTTGWSVFVS SKRLVAGDAF IFLRGESGEL RVGVRRLMRQ VNNMPSSVIS  240
SHSMHLGVLA TASHAISTGT LFSVFYKPRT SRSEFVVSVN KYLEAKKQNL SVGMRFKMRF  300
EGDEAPERRF SGTIIGIGSV PAMSKSPWAD SDWKSLKVQW DEPSAIVRPD RVSPWELEPL  360
DASNPQPPQP PLRNKRARPP ASPSVVAELP PSFGLWKPPS EAAQTLSFSE PQRAREIFPS  420
IPASIFSASS HVEFNSKNEP SILSNQFYWS MRDSKTDSFS ASTNKTRVER KQEPTTMGCR  480
LFGIEISSAV EEALPAATVS GVGYDQTVLS VDVDSDQISQ PSNGNKSDAP GTSSERSPLE  540
SQSRQVRSCT KVIMQGMAVG RAVDLTKLNG YGDLRSKLEE MFDIQGDLCP TLKRWQVVYT  600
DDEDDMMLVG DDPWDEFCSM VKRIYIYSYE EAKLLAPKSK LPVIGDTIKL SSMNSSHESV  660
DLDNHASVTN RDC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.013621357Auxin response factor 1
4ldw_A0.013621357Auxin response factor 1
4ldw_B0.013621357Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.170700.0callus| flower| leaf| panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329749430.0
Expression AtlasQ0JCZ4-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, leaves and young panicles. {ECO:0000269|PubMed:17408882}.
Functional Description ? help Back to Top
Source Description
UniProtAuxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g36054.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g36054
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0649250.0AK064925.1 Oryza sativa Japonica Group cDNA clone:J013000N16, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636800.10.0auxin response factor 9 isoform X3
SwissprotQ0JCZ40.0ARFI_ORYSJ; Auxin response factor 9
TrEMBLI1PLK10.0I1PLK1_ORYGL; Auxin response factor
STRINGOS04T0442000-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP108236116
Representative plantOGRP5501582
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G59750.40.0auxin response factor 1
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Wang D, et al.
    Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa).
    Gene, 2007. 394(1-2): p. 13-24
    [PMID:17408882]